Looks like I was wrong about using an established character for the sake of brevity. Goodwin says in the intro that he had been reading Manhunter reprints in the back of whatever New Gods comics were coming out at the time, and liking it. He said he liked the idea of "man as the most dangerous game" and had liked the Manhunter name. When he started work on his new ninja storyline he said he wanted to pay homage to Paul Kirk by giving his new character one of those two names, Paul or Kirk, but couldn't find a better name to pair with either of them and just stuck with Paul Kirk. Since he borrowed the name he eventually got around to linking his new character to the Golden Age Manhunter.

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I was confused and certain things didn't seem to make sense to me. The main one being that Paul Kirk (The Manhunter.) is supposed to have super strength, but it seems very plot-based. For example, he gets shot at quite a few times, but shouldn't he be impervious to it?

He has a healing factor. He can be injured but his injuries will heal quickly. His mentor Asano Nitobe says "So, you are not invulnerable. But if the injury is not to the heart or head ... the probability is that you shall survive."

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What was the deal with that helmet thing that Dr. Markos had on at the end?

The Council is made up of the ten most brilliant minds on Earth, working together to save mankind from its own destructive tendencies. In order to live long enough to see the fruits of their efforts, they have cryogenically preserved themselves. At any given time only one member is active, and aging, while the rest remain ageless in suspended animation. The helmet allows the active member (currently Dr. Mykros) to access the brain power of (or maybe talk to?) the other nine. Later in the story he says he can also link his mind to the Council's computer and control all defenses and base systems himself.

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Why didn't anyone else seem to want to stop or question the Counsel?

I think the Council had been operating in secret and nobody knew about them except Catherine St. Clair until Kirk started his public vendetta.

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Why did Batman just like The Manhunter walk away after he just killed a guy right in front of him?

I'm not sure how out of character that was. Basically the man Kirk killed was an assassin who was just about to kill Batman. Batman says that regardless, Kirk is a murderer. Kirk says there are many more assassins where that guy came from and only he could stop them. Batman decides to work with Kirk to disable the threat. He may have brought Kirk to justice after the story was over, if Kirk hadn't died at the end.

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And why did they choose to resurrect Kirk anyway?

Dr. Mykros says that Kirk rescued him from Nazis in '45. I assume that, plus the fact that Kirk was a good physical specimen to sample for cloning made him a good choice.

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I also thought that his death could have been a little bit more poignant. But I am glad that I read this, and there were some good parts to this, as well as some poignant moments and some good characterization.

It was a bit abrupt, to be sure. Who knew he had a plan to self-destruct the Council base until the last page and a half? I guess when you have a limited page count some things get rushed.